def main_align(args, stdout, stderr) :
if args.outDir is None :
args.outDir = "."
for fastaFile in args.input :
pyalign.ungapFastaFile(fastaFile, fastaFile + ".ungap.tmp")
pyalign.runMafft(fastaFile + ".ungap.tmp", fastaFile + ".tmp", args.nthreads)
out = os.path.join(args.outDir, os.path.basename(fastaFile))
os.rename(fastaFile + ".tmp", out)
os.remove(fastaFile + ".ungap.tmp")
def test_run_000(self) :
mod.runMafft("inputToto", "outputToto", 4)
result = self.command
expected = "mafft --thread 4 inputToto | awk '{if (substr($0,1,1)==\">\"){if (p){printf \"\\n\";} print $0} else printf(\"%s\",$0);p++;} END {print \"\\n\"}' > outputToto"
self.assertEqual(result, expected)